Detection and identification of lampreys in Great Lakes streams using environmental DNA

Control of sea lamprey Petromyzon marinus in the Great Lakes requires accurate assessment of the instream distribution of this pest species and the ability to distinguish it from the four lamprey species that are native to the Great Lakes (American brook lamprey Lethenteron appendix, chestnut lamprey Ichthyomyzon castaneus, northern brook lamprey Ichthyomyzon fossor, and silver lamprey Ichthyomyzon unicuspis). We developed PCR-based environmental DNA (eDNA) assays to distinguish among the four “genetic species” of Great Lakes lampreys (silver and northern brook lampreys were genetically indistinguishable), tested them under laboratory conditions, and demonstrated in the field that both spawning and larval sea lamprey can be detected using eDNA. In the laboratory, mean detection frequency decreased with increasing flow rate, but was not significantly related to larval density or temperature over the range of relatively high densities tested. Proof-of-concept was demonstrated in the field when sea lamprey eDNA was detected during the spawning season (when large-bodied adults, their gametes, and later their carcasses were present); sampling effort involved collection of three 1-2 L water samples at each of four transects (0.4-1.0 km apart). Mean detection frequency remained high (81-97%) until spawning ceased at the end of June, but decreased thereafter, falling to 6% by mid-August. We also demonstrated that eDNA of smaller, burrowing larvae (in water collected after mid-August) was detectable in two of four streams with medium to high larval density (1-2 larvae/m2), but not at low densities (< 0.1 larvae/m2), potentially due to the exacerbating effect of high flow rates.